scholarly journals The Use of Connected Masks for Reconstructing the Single Particle Image from X-Ray Diffraction Data. III. Maximum-Likelihood Based Strategies to Select Solution of the Phase Problem

2017 ◽  
Vol 12 (2) ◽  
pp. 521-535 ◽  
Author(s):  
Н.Л. Лунина ◽  
N.L. Lunina
Keyword(s):  
Bragg Diffraction ◽  
Biological Macromolecules ◽  
Phase Problem ◽  
X Ray Diffraction ◽  
Additional Advantage ◽  
X Ray ◽  
Experimental Limitation ◽  
New Criterion ◽  
Selection Of

The main experimental limitation of biological crystallography is associated with the need to prepare the object under study in the form of a single crystal. New powerful X-ray sources, namely free-electron X-ray lasers, makes it possible to raise the question of the determination of the structure of isolated biological macromolecules and their complexes in practice. An additional advantage of working with isolated particles is the possibility to obtain information about scattering in all directions, and not only in those limited by the Laue-Bragg diffraction conditions. This significantly facilitates the solution of the phase problem of X-ray diffraction analysis. This paper is devoted to two lines of development of the method for solving the phase problem, proposed earlier by the authors, which is based on the random scanning of the configuration space of potential solutions of the phase problem. The paper suggests a new criterion for the selection of "candidates" for solving the phase problem in the process of scanning. It involves the maximization of statistical likelihood, and its effectiveness is shown in test calculations. The second line concerns the choice of the optimal scanning strategy. It is shown that the gradual expansion of the set of experimental data used in the work allows obtaining solutions of a higher quality than those obtained with all available data included into the work simultaneously from the beginning.

The biological crystallography without crystals

2017 ◽  
Vol 12 (1) ◽  
pp. 55-72 ◽  
Author(s):  
В.Ю. Лунин ◽  
V.Y. Lunin
Keyword(s):  
Three Dimensional ◽  
Scattering Data ◽  
Dimensional Structure ◽  
Biological Macromolecules ◽  
X Ray Diffraction ◽  
X Ray ◽  
Biological Objects ◽  
Standard Problem ◽  
Problems And Solutions

The main obstacle to the determination of the atomic structure of a biological macromolecule by X-ray structural analysis is the need to obtain a crystal of the object under study. This need is due to the complexity of the experimental registration of scattering from a separate molecule. However, it is not always possible to get crystals of biological objects. The development of experimental techniques, in particular the emergence of the X-ray free-electron lasers, allows to approach the practical solution of the problem of registration of the scattering from an isolated particle and thereby to obtain information about the three-dimensional structure of non-crystalline biological objects by X-ray diffraction methods. Sampling of experimental scattering data makes the task of the structure determination of a single particle equivalent to the standard problem of biological crystallography, which allows to extend the biological crystallography techniques to the study of isolated biological particles (individual cells, organelles, molecular machines and, in the future, biological macromolecules). This article is devoted to the state of the art in this area, problems and solutions.

scholarly journals Determination of the Structure of Biological Macromolecular Particles Using X-Ray Lasers. Achievements and Prospects

2020 ◽  
Vol 15 (2) ◽  
pp. 195-234
Author(s):  
T.E. Petrova ◽  
V.Y. Lunin
Keyword(s):  
Single Molecule ◽  
Experimental Approach ◽  
Biological Macromolecules ◽  
X Ray Diffraction ◽  
X Ray ◽  
Current State ◽  
Fundamental Possibility ◽  
Diffraction Patterns ◽  
Further Development

X-ray diffraction analysis is the main experimental approach to determining the atomic structure of biological macromolecules and their complexes. The most serious limitation of its applicability, to date, is the need to prepare a sample of the object under study in the form of a single crystal, which is caused by the extremely low intensity of rays scattered by a single molecule. The commissioning of X-ray Free-Electron Lasers with their super-powerful (by many orders of magnitude exceeding the brightness of modern synchrotrons) and ultra-short (less than 100 fs) pulse is an experimental breakthrough that allows us to expect to obtain diffraction patterns from individual biological particles and then determine their structure. The first experimental results demonstrate the fundamental possibility of such an approach and are accompanied by the publication of a significant number of articles on various aspects of the development of the method. The purpose of this article is to discuss the current state of art in this area, evaluate the results achieved and discuss the prospects for further development of the method based on the analysis of publications in the world scientific literature of recent years and the experience of work carried out by the review authors and their colleagues.

scholarly journals X-ray diffraction by surface acoustic waves

2021 ◽  
Vol 54 (1) ◽  
pp. 180-194
Author(s):  
Dmitry Roshchupkin ◽  
Luc Ortega ◽  
Olga Plotitcyna ◽  
Ivo Zizak ◽  
Simone Vadilonga ◽  
...  
Keyword(s):  
Acoustic Waves ◽  
Surface Acoustic Waves ◽  
Bragg Diffraction ◽  
Total External Reflection ◽  
X Ray Diffraction ◽  
Rocking Curve ◽  
X Ray ◽  
Diffraction Region ◽  
First Time

The possibilities are presented of X-ray diffraction methods for studying the propagation of surface acoustic waves (SAWs) in solids, including diffraction under total external reflection conditions and Bragg diffraction, using acoustically modulated X-ray multilayer mirrors and crystals. SAW propagation was studied using both meridional and sagittal diffraction geometries where the SAW wavevectors and X-ray photons are collinear or perpendicular, respectively. SAW propagation in a crystal leads to sinusoidal modulation of the crystal lattice and the appearance of diffraction satellites on the rocking curve. The intensities and angular positions of these diffraction satellites are determined by the SAW wavelength, amplitude and attenuation. Therefore, diffraction methods allow the analysis of the SAW propagation process and determination of SAW parameters. The influence of X-ray energy on diffraction by acoustically modulated crystals is studied for the first time. It is shown that changes in the X-ray energy can change the angular region where diffraction satellites exist under conditions of total external reflection. By contrast, in the Bragg diffraction region changes in the X-ray photon energy lead to changes in the X-ray penetration depth into the crystal and redistribution of the diffracted intensity among diffraction satellites, but do not change the angular divergence between diffraction satellites on the rocking curve. It is also shown that, in X-ray diffraction on acoustically modulated crystals on a number of successive reflections, a decrease in interplanar spacing leads to an increase in the number of diffraction satellites and a redistribution of diffracted radiation between them.

scholarly journals Transmission electron microscopy for the evaluation and optimization of crystal growth

2016 ◽  
Vol 72 (5) ◽  
pp. 603-615 ◽  
Author(s):  
Hilary P. Stevenson ◽  
Guowu Lin ◽  
Christopher O. Barnes ◽  
Ieva Sutkeviciute ◽  
Troy Krzysiak ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Transmission Electron Microscopy ◽  
Biological Macromolecules ◽  
X Ray Diffraction ◽  
Tem Analysis ◽  
X Ray ◽  
X Ray Crystallography ◽  
Transmission Electron ◽  
Selection Of ◽  
Qualitative Estimation

The crystallization of protein samples remains the most significant challenge in structure determination by X-ray crystallography. Here, the effectiveness of transmission electron microscopy (TEM) analysis to aid in the crystallization of biological macromolecules is demonstrated. It was found that the presence of well ordered lattices with higher order Bragg spots, revealed by Fourier analysis of TEM images, is a good predictor of diffraction-quality crystals. Moreover, the use of TEM allowed (i) comparison of lattice quality among crystals from different conditions in crystallization screens; (ii) the detection of crystal pathologies that could contribute to poor X-ray diffraction, including crystal lattice defects, anisotropic diffraction and crystal contamination by heavy protein aggregates and nanocrystal nuclei; (iii) the qualitative estimation of crystal solvent content to explore the effect of lattice dehydration on diffraction and (iv) the selection of high-quality crystal fragments for microseeding experiments to generate reproducibly larger sized crystals. Applications to X-ray free-electron laser (XFEL) and micro-electron diffraction (microED) experiments are also discussed.

Sem and X-Ray Analysis of Renal and Biliary Calculi

1976 ◽  
Vol 34 ◽  
pp. 306-307
Author(s):  
R. J. Narconis ◽  
G. L. Johnson
Keyword(s):  
Chemical Constituents ◽  
Natural State ◽  
X Ray Diffraction ◽  
Chemical Methods ◽  
X Ray ◽  
Additional Dimension ◽  
Biliary Calculi ◽  
Calculus Formation ◽  
Scanning Electron

Analysis of the constituents of renal and biliary calculi may be of help in the management of patients with calculous disease. Several methods of analysis are available for identifying these constituents. Most common are chemical methods, optical crystallography, x-ray diffraction, and infrared spectroscopy. The application of a SEM with x-ray analysis capabilities should be considered as an additional alternative.A scanning electron microscope equipped with an x-ray “mapping” attachment offers an additional dimension in its ability to locate elemental constituents geographically, and thus, provide a clue in determination of possible metabolic etiology in calculus formation. The ability of this method to give an undisturbed view of adjacent layers of elements in their natural state is of advantage in determining the sequence of formation of subsequent layers of chemical constituents.

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